In the letter, DeSisto says a third-party investigation by Travelers Casualty & Surety Co. concluded that Connor misappropriated $537,988.68 during his tenure as CEO of MaineToday Media from June 2009 to October 2011, when he resigned citing personal reasons.

As a result of that investigation, Travelers has returned that amount, minus a $50,000 deductible, to MaineToday Media under the company’s employee theft insurance policy. DeSisto, a veteran of The Boston Globe who took the reins at MaineToday Media in November 2012, said the money has been reinvested in the company.

Connor, a Bangor native and current resident of Falmouth, disputes the claims.

In a phone call Wednesday evening, Connor said DeSisto’s letter is “erroneous throughout.”

“It’s inaccurate, we dispute it and we’ve been disputing it for a long time,” he said.

Connor, who led an investment group that acquired MaineToday Media in June 2009, claims the whole thing is a misunderstanding that stemmed from him working without a contract and the lack of a system for authorizing expenditures related to his moving to Maine to take the CEO job.

DeSisto’s letter suggests that the company and its board — after hiring a “trusted CFO” and “several independent forensic accounting reviews” — initiated the investigation, though Connor claims he was the one who brought up the accounting issues in October 2011.

“There has been an ongoing issue about who owed who what and how much,” Connor told the Bangor Daily News. “And I raised this question with the investors and the board. The company didn’t. I raised it in October 2011 because we had been unable to get clear answers from the CFO of the company and our auditors. This was all instigated by me, no one else. We had an agreement, a verbal agreement, to have accountants working for me and accountants working for the company to try to sort out a tangled set of financials that involved several newspapers.”

Connor claimed that after he left MaineToday Media, the company refused to sit down with him to settle the matter — “and this is the result,” he said.

Thomas Fitzpatrick, an attorney for Boston-based firm Davis Malm D’Agostine, which is representing MaineToday Media, challenges Connor’s explanation of the situation and his claims that he tried to resolve the problem beforehand.

“It’s very easy to resolve that: You give the money back,” Fitzpatrick said.

He continued: “He can’t dispute that a third party, Travelers Insurance, that doesn’t take sides — they’re guided by what are the facts — looked at and concluded Mr. Connor misappropriated half a million dollars.”

Peter Bennett, Connor’s lawyer, said they were exploring their legal options in the wake of the allegations.

“I feel pretty confident he has legal options, but we haven’t had any time to decide what to do,” said Bennett, who was reached on his cellphone while driving on I-90 through Massachusetts.

DeSisto’s letter detailed the $537,988.68 the company is alleging Connor stole down to the penny.

• $36,089.74 in unauthorized compensation for and use of company automobiles, including the purchase of a new Chevy Suburban for his son three days after he started at MaineToday Media.

• $22,940.35 in unauthorized hand-written checks drafted by or at the direction of Connor for items including home landscaping, personal dental work and a $6,000 Camden vacation rental.

• $16,000 in unauthorized use of company funds to pay for another Camden vacation rental.

• $10,000 in an unauthorized wire transfer to Richard Connor.

• $5,000 in claim expenses.

Connor would not address each item, except to say some of them — such as the dental work — were related to health insurance claims and others — the Camden vacation rentals — were related to living expenses incurred when he first moved to Maine to take over as CEO.

“These things look pretty salacious, but it’s not what it appears, and I’m totally confident telling you that,” Connor said.

Connor accused the News Guild of Maine of instigating the allegations made against him. The guild represents 200 employees at the Portland Press Herald and Morning Sentinel, according to the Press Herald.

“I think when you get to the end of that story and hear Tom Bell and the News Guild, you get another glimpse into what motivated this,” Connor said, referring to the article published in the Portland Press Herald.

Tom Bell, president of the guild, could not be reached for comment on Wednesday evening.

This is not the first time Connor has been accused of fiscal infractions.

In May 2012, Wilkes-Barre Publishing, the parent company of The Times Leader, a newspaper in Wilkes-Barre, Pa., sued Connor over allegations that he failed to repay more than $250,000 in loans the company made to him, according to court records. Connor was editor and publisher of The Times Leader from April 2006 to October 2011, when he resigned at the same time he did from MaineToday Media.

Connor disputes the allegations leveled against him by Wilkes-Barre Publishing.

MaineToday Media has no plans to pursue litigation against Connor, Fitzpatrick said.

There is, however, the potential that Travelers could pursue litigation to recoup the funds it has reimbursed to MaineToday Media, Fitzpatrick said.

“In the insurance world they now own that claim against Mr. Connor and what they do with it is up to them,” he said. “But for MaineToday Media — they’re hoping to put the Rich Connor era firmly behind them.”

Patrick Linehan, a spokesman for Travelers, declined to comment on the company’s intentions regarding litigation against Connor.

Bennett, Connor’s lawyer, said he would “be surprised” if Travelers pursued litigation.

Asked to elaborate, he said, “Let’s put it this way, there’s two sides to every story. Travelers hasn’t heard the second side yet, but they will.”